S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

Biomedical research is set to greatly benefit from the use of
semantic web technologies in the design of computational
infrastructure. However, beyond well defined research initiatives,
substantial issues of data heterogeneity, source distribution, and
privacy currently stand in the way towards the personalization of
Medicine.

A computational framework for bioinformatic infrastructure was
designed to deal with the heterogeneous data sources and the
sensitive mixture of public and private data that characterizes the
biomedical domain. This framework consists of a logical model build
with semantic web tools, coupled with a Markov process that
propagates user operator states. An accompanying open source
prototype was developed to meet a series of applications that range
from collaborative multi-institution data acquisition efforts to
data analysis applications that need to quickly traverse complex
data structures. This report describes the two abstractions
underlying the S3DB-based infrastructure, logical and numerical, and
discusses its generality beyond the immediate confines of existing
implementations.

Conclusions: The emergence of the "web as a computer"
requires a formal model for the different functionalities involved
in reading and writing to it. The S3DB core model proposed was found
to address the design criteria of biomedical computational
infrastructure, such as those supporting large scale
multi-investigator research, clinical trials, and molecular
epidemiology